Search for NUMODs in your protein or DNA sequence
A Little about nuclease-associated modular DNA-binding domains - NUMODs
We have identified four new types of short conserved sequence domains in homing endonucleases and related proteins. These domains are modular, appearing in various combinations. One domain includes a motif known by structure as a novel sequence-specific DNA-binding helix. Sequence similarity shows two other domains to be new types of HTH DNA-binding domains. We term the new domains nuclease-associated modular DNA-binding domains (NUMODs).
We have published these domains see: "Sitbon,E.&Pietrokovski,S.(2003).New types of conserved sequence domains in DNA-bindin regions of homing endonucleases.Trends Biochem.
Sci.28,473-477".
A preprint of this paper.
These multiple sequence alignments have been deposited with the European Bioinformatics
Institute (fttp:/ftp.ebi.ac.uk/pub/databases/embl/align) with accession numbers: NUMOD1, ALIGN_000570; NUMOD2, ALIGN_000571; NUMOD4a, ALIGN_000574; NUMOD4b, ALIGN_000575; NUMOD4c, ALIGN_000576.
NUMOD1, NUMOD3, and NUMOD4, can be found in InterPro as well.
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The I-TevI protein contains NUMOD3 in its DNA binding region. The structure of the DNA binding region was previously determined (Van Roey, P. et al. (2001) Embo J 20, 3631-7.). In the following page you can find figures of I-TevI (pdb code 1i3j) with NUMOD3 highlighted.
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Latly, NUMOD4 (A,B and C) were identified as DNA binding motifs by:
Betty W. Shen, Markus Landthaler,David A. Shub and Barry L. Stoddard
as published in" (2004) DNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI JMB 342(1).43-56 "
See link
See link
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This project was created by Einat Sitbon and Dr. Shmuel Pietrokovski
Department of Molecular Genetics,the Weizmann Institute of Science, Rehovot, Israel
Web implementation based on the work of
Dana Reichman
Department of Molecular Genetics,the Weizmann Institute of Science, Rehovot, Israel
Web implementation based on the work of Dana Reichman